Chlamydiae Genomes Re-Annotation Initiative

Redesign of the initiative in 2015

Few months after the CBRS meeting 2013 and our agreement about a general procedure the situation changed significantly. The NCBI announced their plans to re-annotate all prokaryotic genomes in their RefSeq database. Despite the surprise this was very good news, as we can now join forces with the NCBI, utilize their sophisticated infrastructure and thus reduce the workload on our side.

In 2014 we met several times with the colleagues from NCBI RefSeq, have discussed our aims and their plans. The NCBI is very nterested to collaborate with our initiative, which will also be sort of a pilot project for other organisms. We can now propose an updated procedure for the re-annotation of the chlamydial genomes:

2) Contributions requested from us:
- Definition of reference genomes: The RefSeq team requests the definition of reference genomes by the community. These should be the genome(s) of a species, for which most literature and functional data exists.
- Manual re-annotation of reference genomes: The RefSeq team requests the improvement of the automatic PGAP-annotations of the reference genomes by the community. Improvements should be based on literature reference and include existence of genes as well as their names and product descriptions.
- Maintenance of re-annotation of reference genomes: To keep high quality of the reference genome annotations, the NCBI requests regular updates (e.g., every year or every 2nd year).

Meeting of the Chlamydiae Genomes Re-Annotation Initiative at the 2015 CBRS meeting in New Orleans

Archive: initial setup of the project in 2013

At the 2013 meeting of the Chlamydia Basic Research Society (CBRS) an initiative for the re-annotation of all chlamydiae genomes has formed. The genomes database, so far residing under this URL, stays online but will permanently become part of this initiative. This site will now host all information and data of the initiative. The genomes database will provide direct access to all re-annotated genomes in any phases of the re-annotation project.

Motivation and concept:

The information about Chlamydiae genomes in the public databases is partially outdated and does not reflect the state of the art in Chlamydiae research. This problem is now really hampering compara­tive analyses, particularly in functional genomics and genetics.

The Chlamydiae Genomes Re-annotation Initiative aims for a community-based re-annotation of all publicly available Chlamydiae genomes. It should be submitted as such to the public databases, re­placing the original annotations. Thereby the whole Chlamydiae research community will bene­fit from up-to-date data e.g. provided by sequence similarity searches and genome data­bases. Furthermore, up-to-date public databases will substantially improve and facilitate future Chlamydiae genome sequencing projects.

Specifically adapted bioinformatic tools will provide a high-quality automatic re-annotation of all publicly available Chlamydiae genomes. This software implements a weighted data integration strategy similar to manual curation. Such re-annotation will not change the numbering (locus tags) of all genes already present in the original annotation (e.g., CT858 will get the gene name CPAF but will keep the locus tag CT858). Manual refinement by the Chlamydiae research community will only need to incorporate specific knowledge from recent literature (and e.g. large-scale omics experiments), and will handle nomenclature issues.

All Chlamydiae researchers are invited to support this initiative and to share their knowledge with the community. Participation will be easy, efficient and adjustable to your availability. All participants will be co-authors on the publication in the end of the project.

In order to sustain database quality, we suggest repeating the re-annotation in regular intervals (e.g. synchronized with the biennial CBRS meetings).

Manually refine annotations (it has been suggested that M2 should be limited to those who volunteer to annotate whole groups of genes)

M3

Provide refined genomes from M2

Manually refine annotations

M4

Provide refined genomes from M3

Manually refine annotations

M5

Provide refined genomes from M4

Submit re-annotation to public databases (NCBI/EMBL/DDBJ)

M6

Provide pan-genome data and analysis; draft manuscript

Contribute to manuscript

Contribute to manuscript

Fin

Submit manuscript

Participate! Join the mailing list:

A mailing list has been created for the Chlamydiae Genomes Re-Annotation Initiative. All relevant information and discussion of the initiative will be communicated via this list. It is technically hosted by the University of Vienna.